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pbg-ld: Linked Data Platform for Plant Breeding & Genomics

DOI Published in PeerJ CI

The pbg-ld software provides access to semantically integrated geno- & pheno-typic data on Solanaceae species (such as tomato and potato) and enables ranking of candidate genes associated with traits of interest.

Prerequisites

Install & deploy

1. Clone this repository.

git clone https://github.com/candYgene/pbg-ld.git

2. Start Docker service(s).

cd pbg-ld
# list available services
docker-compose config --services
# start all services or one-by-one
docker-compose up -d # or add [SERVICE]

Alternatively, deploy the services on a remote server using Ansible Playbook.

ansible-playbook -i inventory playbook.yml

Note: grlc API can be deployed with SPARQL queries stored

  • locally (in the container)
git clone https://github.com/candYgene/queries.git
docker cp queries grlc:/home/grlc/
  • remotely (in a GitHub repo)

Set the environment variables in docker-compose.yml:

  • GRLC_GITHUB_ACCESS_TOKEN
  • GRLC_SERVER_NAME (or CNAME, excluding URI scheme http(s)//:)
  • GRLC_SPARQL_ENDPOINT

3. Access (meta)data in RDF.

Overview of datasets

RDF graphs:IRIs (A-Box)

  • SGN:
    • http://solgenomics.net/genome/Solanum_lycopersicum
    • http://solgenomics.net/genome/Solanum_pennellii
    • http://solgenomics.net/genome/Solanum_tuberosum
  • Ensembl:
    • http://plants.ensembl.org/Solanum_lycopersicum
    • http://plants.ensembl.org/Solanum_tuberosum
  • UniProt:
    • http://www.uniprot.org/proteomes/Solanum_lycopersicum
    • http://www.uniprot.org/proteomes/Solanum_tuberosum
  • QTLs: http://europepmc.org

RDF graphs:IRIs (T-Box)

  • FALDO: http://biohackathon.org/resource/faldo.rdf
  • SO[FA]: http://purl.obolibrary.org/obo/so.owl
  • SIO: http://semanticscience.org/ontology/sio.owl
  • RO: http://purl.obolibrary.org/obo/ro.owl
  • GO: http://purl.obolibrary.org/obo/go.owl
  • UniProt Core: http://purl.uniprot.org/core/
  • PO: http://purl.obolibrary.org/obo/po.owl
  • TO: http://purl.obolibrary.org/obo/to.owl
  • SPTO: http://purl.bioontology.org/ontology/SPTO
  • PATO: http://purl.obolibrary.org/obo/pato.owl